Bio::DB::RefSeq(3) User Contributed Perl Documentation Bio::DB::RefSeq(3)NAMEBio::DB::RefSeq - Database object interface for RefSeq retrieval
SYNOPSIS
use Bio::DB::RefSeq;
$db = Bio::DB::RefSeq->new();
# most of the time RefSeq_ID eq RefSeq acc
$seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID
print "accession is ", $seq->accession_number, "\n";
# or changeing to accession number and Fasta format ...
$db->request_format('fasta');
$seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC
print "seq is ", $seq->seq, "\n";
# especially when using versions, you better be prepared
# in not getting what what want
eval {
$seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
};
print "accesion is ", $seq->accession_number, "\n" unless $@;
# or ... best when downloading very large files, prevents
# keeping all of the file in memory
# also don't want features, just sequence so let's save bandwith
# and request Fasta sequence
$db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
-format => 'fasta');
my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );
while( my $seq = $seqio->next_seq ) {
print "seqid is ", $seq->id, "\n";
}
DESCRIPTION
Allows the dynamic retrieval of sequence objects Bio::Seq from the
RefSeq database using the dbfetch script at EBI:
http://www.ebi.ac.uk/cgi-bin/dbfetch
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
The functionality of this module is inherited from Bio::DB::DBFetch
which implements Bio::DB::WebDBSeqI.
This module retrieves entries from EBI although it retrives database
entries produced at NCBI. When read into bioperl objects, the parser
for GenBank format it used. RefSeq is a NONSTANDARD GenBank file so be
ready for surprises.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and
data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR - Heikki Lehvaslaiho
Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
perl v5.14.1 2011-07-22 Bio::DB::RefSeq(3)